Browse
Submit Data
Databases
API
Help

Dataset Information

21 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome of an endangered orchid Paphiopedilum spicerianum.

ABSTRACT: Paphiopedilum spicerianum (H. G. Reichenbach) Pfitzer is an endangered and threatened orchid species in China. The genetic and molecular data of this orchid species is deficient. With the aim to identify appropriate chloroplast markers for the use in a conservation biology study, the complete chloroplast genome of P. spicerianum was reported. We found that the chloroplast genome of P. spicerianum is 157,292 bp in length, containing a large single-copy region of 87,252 bp, a small single-copy region of 1828 bp, and a pair of inverted repeats of 34,106 bp. Genome annotation predicted 105 unique genes, including 71 protein-coding genes, 30 tRNAs, and four rRNAs. Fourteen genes contained one intron and two genes (clpP and ycf3) had two introns. The GC content of the P. spicerianum was 35.8%. Phylogenetic analysis indicated P. spicerianum was closely related to P. purpuratum.

SUBMITTER: Ge LP

PROVIDER: S-EPMC7594755 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete chloroplast genome sequences of an endangered orchid species Paphiopedilum parishii (Orchidaceae).

Project description:Paphiopedilum parishii (Rchb. f.) Stein is an endangered and rare species with highly ornamental value. In this study, we report the complete chloroplast genome of P. parishii using the Illumina sequencing data. The total genome of P. parishii is 154,689 bp in length and the GC content is 35.9%, with a pair of inverted repeats (IRs) regions of 32,690 bp each, a large single-copy region (LSC) of 86,863 bp and a small single-copy region (SSC) of 2,446 bp. The chloroplast genome encoded 127 genes, including 82 protein-coding genes (CDS), 8 rRNA genes and 37 tRNA genes. The phylogenetic tree showed that P. parishii was clustered with other species in Paphiopedilum with strong support based on the complete chloroplast genome.

| S-EPMC8330699 | biostudies-literature

Characterization of the complete chloroplast genome of Paphiopedilum micranthum, an Endangered orchid in China.

Project description:Paphiopedilum micranthum is a rare species of terrestrial herb in the Orchidaceae. It is naturally distributed in southwestern China and north of Vietnam. Here, we reported the first complete chloroplast genome (cpDNA) of P. micranthum. The length is 163,243 bp, with 129 genes, including 77 protein coding genes, 38 tRNA genes, and 8 rRNA genes. It includes two inverted repeat regions (IRs) of 36,128 bp each, which were separated by a large single copy region (LSC) of 89,245 bp and a small single copy region (SSC) of 1742 bp. The overall GC-content of the whole chloroplast is 35.8%, while the corresponding values of the LSC, SSC, and IR regions are 33.2, 20, and 39.3, respectively. The complete chloroplast genome sequence of P. micranthum (GenBank accession number: MN535014) can be used as a useful resource for the evolutionary biology study of phylogenetic studies in Orchidaceae.

| S-EPMC7721024 | biostudies-literature

The complete chloroplast genome of the endangered plant Paphiopedilum wardii (Orchidaceae).

Project description:Chloroplast (cp) genome sequences provide a valuable source for phylogenetic analysis, which becomes a popular tool for population and phylogeny in a recent report. Here, the complete chloroplast genome of the Paphiopedilum wardii has been reconstructed from the whole-genome Illumina sequencing data. The circular genome is 169,820?bp in size and comprises a pair of inverted repeat (IR) regions of 33,641?bp each, a large single-copy (LSC) region of 98,872?bp and a small single-copy (SSC) region of 3666?bp. The total GC content is 33.8%, while the corresponding values of the IR regions, LSC, and SSC and are 38.7%, 31.7% and 26.7%, respectively. The chloroplast genome contains 151 genes, including 91 protein-coding genes, eight ribosomal RNA genes and 52 transfer RNA genes. Two genes (ndhA and ndhB) are pseudogenized or lost in its cpDNA. The maximum-likelihood phylogenetic analysis showed a close relationship with P. armeniacum in Orchidaceae. Our findings provide useful information for phylogenetic and evolutionary research of Paphiopedilum species.

| S-EPMC7800172 | biostudies-literature

The complete chloroplast genome sequence of an Endangered orchid species Dendrobium bellatulum (Orchidaceae).

Project description:Dendrobium bellatulum Rolfe is an Endangered orchid species that is distributed in the subtropical regions of Yunnan Province, China. It was listed in the category of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Here, we reported the complete chloroplast (cp) genome sequence and the cp genomic features of D. bellatulum. The genome was 152,107?bp long with 129 genes comprising 83 protein-coding genes, 40 tRNA genes, and 6 rRNA genes. Phylogenetic analysis of a data set of cp genomes indicated that D. bellatulum is clustered with other species in Dendrobium.

| S-EPMC7800090 | biostudies-literature

Complete chloroplast genome of Paphiopedilum emersonii (Orchidaceae).

Project description:Paphiopedilum emersonii is an endemic terrestrial orchid in China. In this study, the chloroplast genome of P. emersonii was determined from BGISEQ-500 sequencing data. The total chloroplast genome was 162,590 bp in length, consisting of a large single-copy region (LSC, 87,852 bp), a small single-copy region (SSC, 870 bp), and two inverted repeat regions (IRA and IRB, 36,934 bp, each). The complete chloroplast genome contains 131 genes, including 81 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. In addition, the phylogenetic analysis indicates that P. emersonii was sister to Paphiopedilum micranthum. The chloroplast genome will contribute to the research and conservation of P. emersonii.

| S-EPMC7783058 | biostudies-literature

The complete chloroplast genome of Paphiopedilum malipoense (Orchidaceae).

Project description:Paphiopedilum malipoense S.C.Chen & Z.H.Tsi is a new orchid species found in Malipo county, Yunnan. Here we report the complete chloroplast (cp) genome sequence and the features of P. malipoense. Its cp genome sequence of P. malipoense is 158,708?bp, including one large single-copy region (LSC, 89,452?bp), one small single-copy region (SSC, 17,692?bp), and two inverted repeat regions (IRs, 25,782?bp). The cp genome encoded 132 genes, of which 112 were unique genes (79 protein-coding genes, 29 tRNAs, and 4 rRNAs). The phylogenetic relationships show that P. malipoense is sister with P. armeniacum-P. wardii.

| S-EPMC7706870 | biostudies-literature

The complete chloroplast genome of Paphiopedilum tranlimianum (Orchidaceae).

Project description:Chloroplast (cp) genome sequences have become a useful tool for phylogeneitc and evolutionary study in recent reports. Here the complete chloroplast genome of the Paphiopedilum tranlimianum has been reconstructed from the whole-genome Illumina sequencing data. The circular genome is 162,127?bp in size, and comprises of a pair of inverted repeat (IR) regions of 31,457?bp each, a large single-copy (LSC) region of 91,711?bp, and a small single-copy (SSC) region of 7,502?bp. The total GC content is 35.4%, while the corresponding values of the LSC, SSC, and IR regions are 32.7%, 26.9%, and 40.9%, respectively. The chloroplast genome contains 133 genes, including 87 protein-coding genes, eight ribosomal RNA genes, and 38 transfer RNA genes. Three genes (ndhA, ndhE, and ndhI) are pseudogenized or lost in its cpDNA. The Maximum-Likelihood phylogenetic analysis showed a close relationship with P. niveum in Orchidaceae. Our findings provide useful information for phylogenetic and evolutionary research of Paphiopedilum species.

| S-EPMC7799620 | biostudies-literature

The complete chloroplast genome sequence of Paphiopedilum purpuratum (Orchidaceae).

Project description:Paphiopedilum purpuratum, an endangered terrestrial orchid distributed in southwestern and south of China. In this study, the complete chloroplast genome (cpDNA) sequence of P. purpuratum was determined from Illumina pair-end sequencing data. With a total length of 158,459?bp in length and includes two inverted repeat regions (IRs) of 34,484?bp each, which were separated by a large single-copy region (LSC) 88,022?bp and a small single-copy region (SSC) 1,469?bp. The chloroplast genome contained 126 genes, including 74 protein conding genes,38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis indicated that P. purpuratum, P. dianthum, P. niveum, P. delenatii, and P. armeniacum cluster together, placed them within genus Paphiopedilum. The complete chloroplast genome sequence of P. purpuratum will provide a useful resource for the evolutionary biology study of phylogenetic studies in Orchidaceae.

| S-EPMC7707658 | biostudies-literature

Complete Chloroplast Genome of Paphiopedilum delenatii and Phylogenetic Relationships among Orchidaceae.

Project description:Paphiopedilum delenatii is a native orchid of Vietnam with highly attractive floral traits. Unfortunately, it is now listed as a critically endangered species with a few hundred individuals remaining in nature. In this study, we performed next-generation sequencing of P. delenatii and assembled its complete chloroplast genome. The whole chloroplast genome of P. delenatii was 160,955 bp in size, 35.6% of which was GC content, and exhibited typical quadripartite structure of plastid genomes with four distinct regions, including the large and small single-copy regions and a pair of inverted repeat regions. There were, in total, 130 genes annotated in the genome: 77 coding genes, 39 tRNA genes, 8 rRNA genes, and 6 pseudogenes. The loss of ndh genes and variation in inverted repeat (IR) boundaries as well as data of simple sequence repeats (SSRs) and divergent hotspots provided useful information for identification applications and phylogenetic studies of Paphiopedilum species. Whole chloroplast genomes could be used as an effective super barcode for species identification or for developing other identification markers, which subsequently serves the conservation of Paphiopedilum species.

| S-EPMC7020410 | biostudies-literature

The chloroplast genome of an Endangered orchid species, Gastrochilus calceolaris (Orchidaceae: Aeridinae).

Project description:This study reported the complete chloroplast genome of a critically Endangered Orchidaceae species Gastrochilus calceolaris and its phylogenetic position in subtribe Aeridinae based on 12 orchid species plastomes. The plastome of G. calceolaris, with a 148,428?bp size, consisted of a pair of inverted repeat regions of 25,950?bp, a small single copy region of 11,139?bp, and a large single copy region of 85,389?bp. G?+?C content was 36.8%. The phylogenetic analysis highly supported the sisterhood between Gastrochilus and Pelatantheria and a monophyletic Gastrochilus group comprising of G. calceolaris, G. fuscopunctatus, and G. japonicus.

| S-EPMC7800495 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data